The distribution of zooplankton biomass and potential metabolic rates, in terms of electron transport system (ETS) and glutamate dehydrogenase (GDH), were analyzed along a cross-shelf transect in waters off Namibia. The highly variable dynamics of upwelling filaments promoted short-term fluctuations in the zooplankton biomass and metabolism. Maximum values were characteristically found over the shelf-break, where zooplankton biomass as dry mass (DM) reached peaks of 64.5 mg m^− 3 within the upper 200 m in late August. Two weeks later, the zooplankton-DM decreased by more than a third (19 mg DM m^− 3). Zooplankton potential respiration and NH₄⁺ excretion averaged 234 μmol O₂ m^− 3 d^− 1 and 169 μmol NH₄⁺ m^− 3 d^− 1 in the Namibian shelf, respectively. High protein-specific ETS activities even in the low-chlorophyll waters outside the filament suggested a shift into greater omnivory seaward. In this light, zooplankton elemental and isotopic compositions were used to investigate the pelagic food web interactions. They evidenced spatial changes in the carbon resource for zooplankton as well as changes in the form of nitrogen that fueled the biological production in aging advected waters. Overall, both aspects of zooplankton metabolism impacted the primary productivity at a level less than 10% under all the different oceanographic conditions. Keywords: Zooplankton, Biomass, Electron transport system (ETS), Glutamate dehydrogenase (GDH), Benguela upwelling system.